Multiple sclerosis (MS) is a common and severe disorder of the central nervous system characterized by chronic inflammation, myelin loss, gliosis, varying degrees of axonal and oligodendrocyte pathology, and progressive neurological dysfunction. MS pathogenesis includes a complex genetic component. In spite of intensive long-standing efforts, the knowledge of MS genetics remains incomplete. Our overall objective is to characterize the repertoire of genes that predispose to MS and modulate its presentation. Their identification is now possible as a result of rapid progress in defining the landscape of genetic organization and cataloging variation across the human genome. This proposal builds on the availability of second generation, high-quality genome-wide association results and comprehensive phenotypic data in a large MS cohort. We propose four main research goals: In Specific Aim 1 high-coverage genome-wide genetic data from a total of approximately 17,000 subjects affected with MS will be pooled and analyzed using a multi-stage and multi- analytical approach to map unambiguous association signals from sequence (SNPs) and copy number (CNVs) polymorphisms and identify novel disease candidate genes, leading to robust and testable hypotheses as to which are the specific common allelic variants conferring susceptibility. Using the meta-analysis-derived genotypes, together with open databases and novel algorithms, we will develop a composite global map of the effects of epistatic interactions and biochemical networks of genomic variation underlying MS pathogenesis. Specific Aim 2 takes advantage of the wealth of phenotypic data available for the different datasets to assess disease course variables and correlations to genotype. Important clinical metrics such as age and site of disease onset, disability at entry of study and progression, and changes in lesion distribution and burden will be incorporated into the analysis of genetic data. This aim directly addresses the question of clinical heterogeneity in MS and the correlation between different phenotypes and genotypes. In Specific Aim 3 we intend to generate high-coverage sequence information for the regulatory regions, exons and flanking regions of genes with unequivocal evidence of association for the discovery of rare variants associated with MS. To efficiently resequence DNA in a large dataset (3,000 patients / 3,000 controls), we will create 120 pools of 50 DNA samples each. Approximately 1,000 low-frequency variants will be genotyped in a validation cohort consisting of 10,000 MS subjects and 10,000 control subjects. As technologies advance and costs retreat, whole exome re-sequencing will be pursued in the second half of the funding cycle. Finally, in Specific Aim 4 we will integrated all the generated data and build an array, the "MS Fine-Mapping Gene-chip," consisting of a comprehensive compendium of common and rare variants covering and flanking confirmed associations with susceptibility and disease expression. All relevant variants will be tested in an independent dataset (10,000 cases / 10,000 controls) for association individually and by combining multiple alleles within a single gene and across multiple genes to assess of causative cumulative effects. From this dataset, we expect to generate a minimal set of DNA variants that individually or in combination can aid in prediction of disease risk and/or progression. The availability of a large and well-characterized cohort as described here, coupled with the aid of high-powered laboratory technologies, provides an outstanding opportunity to identify and characterize MS-related genes. This information may translate into clinically useful genetic biomarkers and reveal novel targets for therapy. PUBLIC HEALTH RELEVANCE: Public Health Relevance Statement Multiple sclerosis (MS) is a common cause of severe neurological disability resulting from the interruption of myelinated tracts in the central nervous system. MS is second only to trauma as a cause of neurologic disability in young adults, affecting approximately 2 million people worldwide and more than 400,000 individuals in the US. Remarkably, the incidence of MS seems to have increased considerably over the last century, and this increase may have occurred primarily in women. The socioeconomic consequences of this long-lasting disease are staggering as 75- 85% of patients are eventually unemployed and at high risk for social isolation. Conservative estimates indicate that this chronic illness results in healthcare costs exceeding $200 billion annually in the United States alone. Thus, MS is the second most costly neurological disorder after Alzheimer's disease. Despite important advances in therapeutics, none of the currently available disease-modifying drugs convincingly alter the long-term prognosis of the disease. Clinical manifestations are extremely diverse, but very little is known about the underlying cause of this variability. It can vary from a benign illness to a rapidly evolving and incapacitating disease. Onset may be abrupt or insidious, and early symptoms may be severe or seem so trivial that a patient may not seek medical attention for months or years. Most patients ultimately experience progressive disability and twenty-five years after onset approximately 80% of affected individuals will require assistance with ambulation. Thus over the long-term, MS is most often a severe disease requiring profound lifestyle adjustments to the affected and their families. We aim to identify the genes and the gene-specific variants that code for products involved in MS susceptibility. We anticipate that there may be several genes involved in MS risk. These genes may work independently or together, and affect susceptibility in concert with environmental factors. Particular combinations of inherited genetic variants may also determine when symptoms develop, or how the disease progresses. Their identification will help to define the basic etiology of MS, improve risk assessment, and influence therapeutics.